<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.Phylo._io</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.Phylo-module.html">Package Phylo</a> :: Module _io </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.Phylo._io-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module _io</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Phylo._io-pysrc.html">source code</a></span></p> <p>I/O function wrappers for phylogenetic tree formats.</p> <p>This API follows the same semantics as Biopython's <a href="Bio.SeqIO-module.html" class="link">SeqIO</a> and <a href="Bio.AlignIO-module.html" class="link">AlignIO</a>.</p> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Phylo._io-module.html#parse" class="summary-sig-name">parse</a>(<span class="summary-sig-arg">file</span>, <span class="summary-sig-arg">format</span>, <span class="summary-sig-arg">**kwargs</span>)</span><br /> Iteratively parse a file and return each of the trees it contains.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Phylo._io-pysrc.html#parse">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Phylo._io-module.html#read" class="summary-sig-name">read</a>(<span class="summary-sig-arg">file</span>, <span class="summary-sig-arg">format</span>, <span class="summary-sig-arg">**kwargs</span>)</span><br /> Parse a file in the given format and return a single tree.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Phylo._io-pysrc.html#read">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="write"></a><span class="summary-sig-name">write</span>(<span class="summary-sig-arg">trees</span>, <span class="summary-sig-arg">file</span>, <span class="summary-sig-arg">format</span>, <span class="summary-sig-arg">**kwargs</span>)</span><br /> Write a sequence of trees to file in the given format.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Phylo._io-pysrc.html#write">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="convert"></a><span class="summary-sig-name">convert</span>(<span class="summary-sig-arg">in_file</span>, <span class="summary-sig-arg">in_format</span>, <span class="summary-sig-arg">out_file</span>, <span class="summary-sig-arg">out_format</span>, <span class="summary-sig-arg">**kwargs</span>)</span><br /> Convert between two tree file formats.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Phylo._io-pysrc.html#convert">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== VARIABLES ==================== --> <a name="section-Variables"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Variables" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Phylo._io-module.html#supported_formats" class="summary-name">supported_formats</a> = <code title="{'newick': <module 'Bio.Phylo.NewickIO' from '/home/mandrake/rpm/BUILD\ /biopython-1.58/Bio/Phylo/NewickIO.py'>, 'nexus': <module 'Bio.Phylo.NexusIO' from '/home/mandrake/rpm/BUILD/b\ iopython-1.58/Bio/Phylo/NexusIO.py'>, 'phyloxml': <module 'Bio.Phylo.PhyloXMLIO' from '/home/mandrake/rpm/B\ UILD/biopython-1.58/Bio/Phylo/PhyloXMLIO.py'>}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">newick</code><code class="variable-quote">'</code><code class="variable-op">: </code><module 'Bio.Phylo.NewickIO' fr<code class="variable-ellipsis">...</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.Phylo'"><code class="variable-quote">'</code><code class="variable-string">Bio.Phylo</code><code class="variable-quote">'</code></code> </td> </tr> </table> <!-- ==================== FUNCTION DETAILS ==================== --> <a name="section-FunctionDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Function Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-FunctionDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="parse"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">parse</span>(<span class="sig-arg">file</span>, <span class="sig-arg">format</span>, <span class="sig-arg">**kwargs</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Phylo._io-pysrc.html#parse">source code</a></span> </td> </tr></table> <p>Iteratively parse a file and return each of the trees it contains.</p> <p>If a file only contains one tree, this still returns an iterable object that contains one element.</p> <div class="rst-section" id="rst-example"> <h1 class="heading">Example</h1> <pre class="py-doctest"> <span class="py-prompt">>>> </span>trees = parse(<span class="py-string">'../../Tests/PhyloXML/apaf.xml'</span>, <span class="py-string">'phyloxml'</span>) <span class="py-prompt">>>> </span><span class="py-keyword">for</span> tree <span class="py-keyword">in</span> trees: <span class="py-more">... </span> <span class="py-keyword">print</span> tree.rooted <span class="py-output">True</span></pre> </div> <dl class="fields"> </dl> </td></tr></table> </div> <a name="read"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">read</span>(<span class="sig-arg">file</span>, <span class="sig-arg">format</span>, <span class="sig-arg">**kwargs</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Phylo._io-pysrc.html#read">source code</a></span> </td> </tr></table> <p>Parse a file in the given format and return a single tree.</p> <p>Raises a <code class="link">ValueError</code> if there are zero or multiple trees -- if this occurs, use <a href="Bio.Phylo._io-module.html#parse" class="link">parse</a> instead to get the complete sequence of trees.</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== VARIABLES DETAILS ==================== --> <a name="section-VariablesDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Variables Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-VariablesDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="supported_formats"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">supported_formats</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">newick</code><code class="variable-quote">'</code><code class="variable-op">: </code><module 'Bio.Phylo.NewickIO' from '/home/mandrake/rpm/BUILD<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> /biopython-1.58/Bio/Phylo/NewickIO.py'><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">nexus</code><code class="variable-quote">'</code><code class="variable-op">: </code><module 'Bio.Phylo.NexusIO' from '/home/mandrake/rpm/BUILD/b<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> iopython-1.58/Bio/Phylo/NexusIO.py'><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">phyloxml</code><code class="variable-quote">'</code><code class="variable-op">: </code><module 'Bio.Phylo.PhyloXMLIO' from '/home/mandrake/rpm/B<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> UILD/biopython-1.58/Bio/Phylo/PhyloXMLIO.py'><code class="variable-group">}</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Thu Aug 18 18:19:21 2011 </td> <td align="right" class="footer"> <a 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